A new lease on life
by ginganinja97
Summary: Michael attempts to leave the hurt from his old life behind him and continue forward. Doing so, he meets some new friends and has some unforeseen adventures.
1. Enter- Michael

**Hello Guys!**

This is a fic that I have based off of my first Pokemon game- XD. In it, Michael is 16 and Ash is just starting out on his adventure (*cringes from necessary spoiler). This is actually my first attempt at taking a story idea and actually putting it on paper so please give me an honest review. Anyways, enjoy!

Please note that I don't own pokemon or any of the stuff related to it. I only use it as a backdrop to my story

* * *

"_One more mission_" Michael kept telling himself "_one more and then you can put this all behind you_".

Ever since he was ten, Michael had been fighting team Cypher and keeping them at bay. Every time he tried to get away from the duty, they rose again and he had to put them down. At he was able to defeat them with pokemon. Nowdays, their tactics forced him to take more drastic measures. Michael shuddered as he remembered what he had been forced to do- and was about to repeat.

"_Don't think about that!_" he scolded himself. "The less you think about it, the easier it will be to accept it". He finished his mental exercising and got together his gear.

As he worked, his partner Jolteon padded into the room looking for attention. Smiling, Michael started to scratch Jolteon behind his ear. "Hey there buddy" he murmured. "You ready to get this over with and start a new life?"

"Jolteon!" his partner exclaimed. Even when he was only an Eevee, Michael kept Jolteon as his first pokemon to battle and the last one to give up. This constant training left him as Michael's most powerful partner.

"Let's get going then" Michael said. He slung his backpack over his shoulder and began to leave when his phone began to ring

"Damn" Michael muttered. "Who is it this time?" Ever since the pokemon G-Men had announced that they were taking over the protection of Orre several months ago, Newspapers and Television Channels had been clamoring for his word on the change of authority. It was proving quite a nusance- especially when he was getting ready for a mission. "Hello?" he asked.

"May I speak to Michael Ryuto?" the female voice asked.

"Speaking" Michael replied

"OMG! MICHAEL!" the voice blared "I KNEW THAT I COULD FIND YOU IF I CALLED EVERY NUMBER IN ORRE'S YELLOW PAGES! Will you marry me?"

Michael slammed the phone down and sighed. Fangirls had been another nuisance ever since he hit puberty and apparently (to the entire female population in Orre besides his mom and sister) became 'hot'. He was starting to think that his sister was selling phone calls to him for the highest bidder.

"Now that I've gotten my daily random fangirl call out of the way, let's get going" Michael told Jolteon

"Jolt!" Jolteon said seriously- all fun and playfulness out of his growl.

Michael slid the snag machine onto his arm and put the Aura reader headset on. He checked the time, only to find to his horror that they had less than 5 minutes to get to the airport- a 20 minute bike, if one followed the speed limits.

"Jolteon! We're running late!"

His companion instantly leapt up off his bed and followed his trainer's mad dash towards the bike. Without pausing to put a helmet on, Michael opened the throttle wide and flew out of the yard and onto the dirt road

* * *

**Okay, for those of you who already read this story before early October 2013 and are rereading this chapter, you might notice that the ending is different. This is because I had the unpleasant duty of editing out a character (if you don't know who that character is, don't worry, just keep reading). I wish I could have kept him in, but he was going nowhere and was one of the reasons I haven't updated in a while. Anyways, enjoy chapter 2!**


	2. En- Route

**Hello once again guys!**

I would like to thank you all for staying with this story so far(despite not really having that many people so far, this is my first story and therefor, any view is a good view right now). In this chapter, we get to the airport and learn more about the mission. Anyways, enjoy!

Oh I almost forgot! [Insert anti- copyright stuff found at the beginning of chapter 1 right here and don't sue me/ take this down]

* * *

Michael barely made it to the plane before it took off.

Barely is, of course, a relative term, decided by the user of the word. For some people, barely would mean getting up the ramp just before it is removed, or fastening your seat belt right as the plane begins to move.

Michael's definition of barely making it is throwing Jolteon into the plane and then diving in after him as it begins to move down the runway- while security officers chased him (possibly due to the bag check table he vaulted).

"Agent 318, reporting for duty." Michael panted.

He looked up to see his current 'boss' Lance exiting the cockpit looking at him in amusement.

"Cutting it a little close there aren't you?" he asked "I was expecting you 15 minutes ago."

"I'm sorry sir, my only excuse is that I lost track of time" Michael gasped.

Lance looked at the young man understandingly. It wasn't the first time Michael had run late due to him readying himself for battle. Frankly, if he himself had been thrown into the situation Michael had been at such a young age, he wasn't sure he would have remained sane.

"One thing sir" Michael asked "why are you here? I thought this was a solo mission."

"There has been, a change of plans" Lance stated. "Cipher has kidnapped a professor who is the leading expert on pokemon relationships as well as a little known disease called 'pokerus'."

Michael was one of the few who knew about it. A year or so ago, Jolteon had been infected with it. It was one of the reasons he was so powerful nowadays.

Lance continued "we theorize that Cipher wants to use pokerus to make their shadow Pokémon even stronger than they are now. I am joining you on this mission because we can't let Cipher get that kind of power. The mission is simple- I will distract the guards while you go in and free the professor and steal as many shadow Pokémon as you can. Once were free, the plane will destroy the base!"

Michael fully understood the hidden meaning within the briefing. If they couldn't get out of there, the plane would destroy the base, and them, and the professor they now had to rescue.

"We'll be over the target in about 15 minutes" Lance said as he returned to the cockpit. "I suggest that you check your gear before that."

Michael unslung his backpack from his back and began looking. At first glance, the backpack looked like what you probably would see a student wearing. That was the ruse that Michael used so that people didn't give him a second glance when he infiltrated secret bases (like the time Cipher set up in the Krabby club in Gaeton Port). Inside, it had everything that you could need for these kinds of missions. It had night vision goggles, lock picks, a hacking device disguised as an MP3 player, first aid kit, combat kife, and a false bottom to hold his Pokémon G- Man issued firearm.

Michael removed the items and opened the false bottom to check the firearm. While they preferred to use less lethal methods of carrying out their missions, every member was issued a berretta M9 9mm. handgun. Carrying 15 rounds per clip and being threaded for a silencer, it was considered one of the best handguns created.

Michael absolutely hated it.

The 9 mm round seemed too small for it to be of any real use to him. He had argued multiple times to Lance that when he got into a firefight, he needed something more powerful. Plus, it just didn't feel right in his hand. The only gun that really did the job was the 1911 he had once picked up from a Cipher peon he had just taken down. Of course, it was immediately confiscated by Lance as soon as he reported back after the mission.

"_Who knows,_" Michael thought "_maybe I'll get lucky again and get one off of another guard!_"

He repacked and went over to Jolteon. The Pokémon was tense and static electricity crackled across his fur. This was a sign that Jolteon was exited for the upcoming battle- even if it could end up as a battle to the death.

"How are you doing buddy?" Michael asked. He would have given him a good scratching, only that was a bad life decision when Jolteon got into what Jovi had affectionately called 'sparky mode'.

"5 minutes 'till" the pilot announced.

Michael started, he had become distracted once again and had lost track of time. Dejectedly, he realize that he wouldn't be able to get some piloting time in. He enjoyed flying the plane once he had gotten all his gear ready and liked talking to the pilot. While he didn't have a pilot's license, (you didn't need one anywhere in Orre) he was very competent and hoped to get one in another region- if he had time of course.

Lance appeared with three parachutes and Michael cringed in anticipation of his phobia. It wasn't that he had a fear of falling; he could look down at any height and only think "wow, that's a long way down".

The truth was that Michael had an irrational fear of _falling_.

"Put these on both of you, and quickly" Lance ordered. "We've barely got 2 minutes before we have to jump!"

Michael laid his down and began to put the smaller one on Jolteon; cringing every time static electricity hit him. He then put the rip- cord in the Pokémon's mouth so that he could pull his own chute. He was about to put his own on when the plane rocked by explosions. Lance and Jolteon hit the side while Michael was thrown into a seat that he desperately grabbed to avoid being thrown around any further.

"What the hell was that?" Lance cried.

"Were hit!" the pilot cried. "Left engine is inoperable and were losing pressure in the cab-"

At that moment the left side of the plane gave an almighty groan as a tear appeared in the side of the plane. The pressure immediately dropped- sucking everything not latched down out the opening along with Lance and Jolteon who had not been able to grab onto something in time.

Michael managed to grab his back pack, but his parachute had already gone out of the plane along with Dunham's memory card that he had put down when he checked his gear.

"Holy sh-!" whatever Lance was about to say through the microphone, it was lost in a rush of wind- not that Michael thought that it was anything nice or worth hearing"

"_I can't believe I'm about to do this"_ Michael thought. He had no choice however and needed to get to the ground. He let go of the seat and jumped out the tear and into the void.

* * *

Chapter 2 guys! In it, we learned that Cypher has kidnapped a professor on Pokerus (comment if you can figure out who it is) and the mission has taken an unexpected turn.

I'd like to thank you for continuing to read this and I hope the cliff- hanger entices you to read more. If you like this, please favorite/ follow it. Also, if you could find some time to give this story a review, I would appreciate it more than anything and I promise to give a shout out to the first person who does- whether it be good or bad (I only ask that you keep it clean, honest, and keep it nice either way). Until next time,

-GN

**Update- this was moved to chapter 2 due to the original chapter 2 having to be cut (which really ticks me off because I spent a large amount of time on that chapter). Anyways, the next chapter will explain why it has taken me so long to update the story and why I have had to do a bit of rewriting. Please review/ favorite/follow and I will see you in the hopefully near future.**

**-GN**


	3. Update

Okay, I'm going to forgo my usual intro since this isn't technically a part of the story, just me apologizing for the delay and giving some information about some changes I've made. Just a FYI this has no bits of the story in it.

First of all, I sadly had to get rid of Dunham. For those of you who are reading this and are looking at the screen like "what the heck is this guy talking about", don't worry about him. He was an AI that I had given Michael as a bit of comic relief for the story. I soon realized that I had nothing in store for him and didn't really see why I should keep him in. I'm sorry for his loss if any of you actually got to like him in the two chapters he was in- I loved him and wish I could keep him in. Trying to put him however, in was holding me down and sort of making me reluctant to post the next chapter.

That brings me into my next thing- I AM SO SORRY FOR LEAVING THIS STORY HANGING! I have a plethora of reasons as to why I haven't updated yet. Just a warning, I'm about to go into "rant mode" and might start sounding a little eccentric during some of it.

First of all, I had to pull the "school comes first" card because Pre- calculus has been kicking my ass in the tests and quizzes. Neither of my first two tests topped 65%, which is really bad considering the teacher makes them worth 70% of your total score. It was only after my last test (which was a 102) did I feel confident enough that I could put some time towards the story.

Also, I spent last weekend at an Order of the Arrow fellowship (for those of you who aren't in boy scouts, a fellowship there is basically a service weekend disguised as a "fun" time thanks to a couple of games saturday afternoon, a spirit award, and a theme for the weekend). My chapter has a completely insane chief (leader) who somehow got us signed up to help with a movie thing about the OA. At first it sounded pretty cool. That was before I spent until 11:30 P.M. reenacting an initiation ceremony while trying to hold my pants up because one of the guys heading it up was in a costume thingy and needed a belt for it. For a picture of what I looked like, imagine a teenage ginger in the middle of the night next to a bonfire surrounded by native Americans, in his class A clothes (the stuff many of you probably think we wear 24/7 on every scout outing even though we don't) desperately trying to hold his pants up, pissed off beyond belief, and just wanting to get into his nice tent and go to sleep since he had spent the last couple of nights worried over the math test he had taken earlier in the day. I then had to walk 30 minutes back to my tent (with my belt thankfully) and crawl into my tent and fall to sleep only to be awoken by my glorious chapter chief who was making a non- mandatory 3k- ish run mandatory, AT 6:30 IN THE MORNING AFTER THE PREVIOUS NIGHT, I MEAN, COME ON DUDE! (FYI due to the stance i'm taking here, you probably think I hate this guy. I don't. I just think he's a little overzealous with spirit and all that at times. I'll be rolling over and going to sleep next time he tries to suggest that.)

Anyways, back to the run. Somehow his guilt tripped me into coming. Halfway through the run, it started raining (I had fortunately brought my rain poncho). It did not stop raining until lunch time and then went back to raining shortly thereafter until midafternoon. One thing you should know about the camp- all of the roads are an orange clay lovingly referred to as "camp ****** asphalt" (I won't say what the camp's name is because you might figure out who I am in my chapter since I am one of two gingers there. Besides, if you were there, these clues should be more than enough to tell you where it is). Needless to say, the clay had turned into the consistency of god knows what. Then we had the ceremony for the new members, the dinner, and the echo show showing what we had done that weekend. By this time I was ready to crawl back into bed when, Surprise! They needed us for a couple more shots for the movie. Sadly I was unable to help them as two of my friends had just gone through their ordeals (the thing you go through to actually get in to the OA) and one of them wasn't feeling well- requiring my other friend and I to walk him back. I know what you are thinking. That's a pretty lame of you GN! However, in my defence, if that guy had passed out, it would have taken both of us to get him back to his tent considering he is a relatively big guy and i'm a relatively weak guy. Then, since we were already there, it seemed a shame to go all the way back to the lodge, so my friend and I crashed in my tent. Sadly the POW WOW (Native American for- hit drum with stick and yell) started soon after that and was conveniently close to my campsite (although, I doubt anyone that side of the nearby military base missed it). Needless to say, that knocked me out for the entire weekend and into the following Monday since I always have trouble adjusting from a sleeping pad back to a tent.

All of that coupled with laziness the reading of other peoples stories on the website, watching funny YouTube videos, dealing with several other story ideas still rushing through my head right now, desperately waiting to get the House of Hades and read it in one night and then rage about the definite cliffhanger of an ending, and the fact that was preparing for my first crack at the SAT I took yesterday (another thrilling rant on the ineptitude of certain individuals in charge of the test and a run in with my chapter chief who fancies himself as a comedian at times) are the reasons I haven't updated in a while. I'd like to continue ranting, but this is starting to look less like an update, and more like a chapter when you look at the length (if you do want to hear my SAT rant, let me know in a review and I'll consider putting it in). just know that I am very sorry, I have not forgotten this story or you faithful readers, and I assure you that the next chapter is underway and I'll have it up as soon as I feel it is worth me posting (I hope to get the mission done in one super long chapter so Michael can get on with his life). Plus, it's getting late and I have school tomorrow. So all in all, I guess I want to say is-

**I'M BACK GUYS! I HAVENT FORGOTTEN ABOUT YOU! EAT LOTS OF BACON! I'LL SEE YOU IN A FEW!**

Remember to favorite this story, or better yet, give it a review! (seriously, if someone could find the kindness in their heart to take some time out of their day to give me a review and tell me their honest opinion of how they think i'm doing, I will love them in a non- gay way unless they are a girl).

**-GN**


	4. Out Of The Frying Pan

**Hey guys!**

**Chapter 3 is finally here! Just a warning- while I didn't manage to get the entire mission into one chapter, it is still extremely long (the longest I've ever written).**

**Also, we hit 2 major milestones between chapters. We topped 100 views, and have our first favorite. Thank you ****Phoenix NightStar! ****I'm pretty excited because this is my first story and I honestly wasn't sure it would take off. From what I'm seeing so far, the opposite is true.**

**FYI, this chapter might get a little graphic and take a dance on the grayed line between the T and M ratings, if you go by the ESRB inspired rating system this website has (which I don't particularly like since I don't like the ESRB very much). However, I believe that this story still deserves the T rating which is how I shall write most, if not all my work. Anyways,,,**

**Roll story!**

* * *

"_I wonder where Professor Oak is"_ Delia Ketchum wondered _"he hasn't been seen for several weeks."_

Without The Professor, her son, Ash, would be unable to start his Pokemon journey. She knew he would be devastated if he couldn't start on his tenth birthday.

Speaking of which, she could hear him coming down the stairs.

"Hey Mom, I've finally decided that I want to start my Journey with a Bulbasaur" Ash cried.

"_wait for it,,,,,,"_

"Hang on, Charmander is pretty strong too, and with an advantage over Bulbasaur,,,," Ash rambled on,

Delia smiled. Her son had been acting like this for the past week, changing his mind every five minutes about which of the three starter Pokemon he would choose. As with most things, he would continue to do so right up until it was time to choose.

"I'd better get back to thinking about it" Ash said. "I want to pick the right one so I can be a Pokemon master!"

Delia turned to the television screen

"breaking news in the Orre region about how a Pokemon League plane crash landed in the desert. The pilot is fine but says that his two occupants fell out of the plane and are nowhere to be seen. We now go live to the ONBS reporter live at the scene."

*0*0*

As usual, as soon as Michael left the plane, his world became eerily quiet- save for the wind whistling in his ears.

"_Brain, quit the fancy wording"_ Michael thought _"focus on the current issue, like, y'now, you are FALLING WITHOUT A FREAKING PARACHUTE!"_

He desperately searched the sky. Fortunately, the -chute was almost directly below him. Unfortunately, the plane had lost a lot of altitude after it was hit. Michael figured he had less than a minute before he hit the ground.

Despite having a morbid fear of falling, Michael had done aerial insertions before and had picked up some skills because of it. He angled himself straight down and began to pick up speed, racing by a startled Lance and Jolteon. Right as he passed by, he grabbed the parachute. He now faced an issue of poor judgment on his part. He had placed his backpack right where the parachute needed to go.

Michael had mere seconds to choose. He instantly knew that in order to survive he would have to sacrifice some, if not all of his gear. He quickly removed his pack and released it, letting it get blown away from him. He quickly donned the parachute and with the pull of the ripcord, heard the satisfying snap of the parachute opening. He was almost too late.

In the time he had taken to put on the parachute, he had come within 10 seconds of the ground. Most professional skydivers agree that less than ten seconds of time with the parachute engaged is not sufficient time to slow down enough to escape physical harm.

Fortunately for Michael, most professional skydivers land on dirt; not the soft sand dune his controlled crash took him into.

Michael was confused. One second he was hurtling towards the ground, the next, he had his face stuck in something hot, gritty, and very dark. As he tried to free himself, he felt a strong hand grab him and roughly yank him out. Good thing Lance had gotten to him.

Michael frowned. He had passed Lance early on in his fall. How had he gotten down so fast?

"Not one move boy" a gruff 'not-Lance's-voice' said. Michael heard the all too familiar sound of the slide of a handgun being drawn back and a round being chambered.

"You've caused far too much trouble for Cipher". The voice said. "A promotion to Admin status is available for the person who brings your head in. The rest of the body isn't required."

"_So this is how it ends_" Michael thought. He had been battling Cipher for nearly 6 years now. It seemed a shame that it culminated into a useless dea-

"DRAGONITE! USE HYPERBEAM!"

The unfortunate guard didn't even have time to cry out as a he was engulfed in a blast of raw power. Michael looked around to find lance floating down on the back of his Dragonite along with Jolteon.

"Jolteon! Are you alright?" Michael called.

"Jolt!" Jolteon replied happily. He was glad to see that his trainer was unhurt. It had been a shock for him to see his trainer fall.

"I'm impressed, Michael" Lance sarcastically said. "We aren't even 5 minutes into the mission and you have already managed to scare Jolteon and I to death with that stunt back there AND nearly get your head blown off by a simple guard".

"I had it all under control." Michael shot back. "Speaking of the guard, where is he?"

They looked around, but except for the pistol and a scorch mark, there wasn't much to show where he had gone.

"Man; I hated to do that, but he left us me no choice". Lance said "let's get your gear back together.

This proved to be easier said than done. The landing had busted the bag open and scattered the gear everywhere. They searched for 5 minutes, but all they could find was a broken memory chip that Michael had left in the bag from a time that the bag served its original purpose..

"Damn; I had all my music and several years of photos." Michael said sadly. "It was really starting to take on a personality"

It was more than just the loss of data or the fact that it had more memory than most home computers available. It had been one of the last things his dad completed- a side project while working on the purifying machine. After he died, it was in his will that Michael got the chip.

"You had to choose between the chip and your life, Michael" Lance said calmly. "Now, however is not the time to feel bad about lost gear. With the plane out of commission, we now have to destroy the base on our own along with the original plan. Without any weapon, however, you won't be of much use in anything past a pokemon battle"

Michael was preparing a comeback about how he could hold his own even without a gun when,

"Jolteon! Jolt!"

Both trainers turned to see Jolteon trotting towards them with the gun from the guard.

"You know, Lance, I think we might have just solved one of those problems."

*0*0*

Michael had hit the jackpot once again. Unlike the Pokemon G- Men, Cipher issued all its soldiers .45 caliber pistols- a choice (according to Michael) that should have been enough of a reason why he should be allowed to keep the 1911 now stuck in his belt.

"_He's doesn't seem ecstatic about it though," _Lance thought sadly, "_right now, he's more of a stone than a person. A Geodude could show more emotion than him right now!"_

Lance felt bad for the young trainer. He had first met Michael 4 years ago when the international community began to notice Orre's plight. Back then, Michael was a spunky, annoying twelve year-old with a large ego that came from taking down a large criminal organization at such a young age. As Cipher began to become more like terrorists, Lance began to see less and less of that young kid who had grown on him.

Growing up in Orre is hard enough. Spending most of your teenage years keeping an evil organization down while dodging obnoxious members of the corrupt 'government' that controlled Orre with an iron fist certainly didn't help. Lance was glad that Michael was leaving for Kanto soon- for his sake.

Michael shook Lance out of his thoughts with a hand signal to stop. They had crested the dune and reached the entrance to Cipher's base

*0*0*

Living proof that the government in Orre is corrupt was the fact that Cipher could keep the same hideout for more than half a decade with just a few bribes here and there to the right politician. It was the same hideout that Michael had rescued Professor Krane from and nearly destroyed on multiple occasions. Cipher just kept slinking back and rebuilding.

Fortunately for Michael and Lance, this meant that it was easy to find the base and take it down again.

"If only the government allowed us to actually do some real damage to the base, we'd have ended this ages ago!" Michael mused. "They keep talking about funding Mom's center to go in and learn more about the actual process of creating shadow Pokemon, but as far as I know, no one from the lab has been contacted by the government for any reason more than to try and bully us into relocating!"

Years ago, they might have had to battle several peons before entering the building. Now, because of the damage that the Pokemon G-Men had caused, there was no one on guard duty.

Michael, Lance, and Jolteon slipped inside the building. The inside was even worse than the dilapidated outside. Rust and debris littered the floor and some of the floor tiles had even broken off to reveal the dirt floor beneath.

"It looks like they can't afford housekeeping" Lance Joked. Michael ignored him and Lance once again reflected on the sad fact that Michael had lost his childh-

The elevator dinged and out came another guard. He barely had time to yell in shock before Michael hit him with the butt of his gun, knocking him unconscious.

Michael hid the guard in a nearby locker and entered the still open elevator before turning back to a stunned Lance.

"Well, are you coming or not?"

"_Then again, losing your childhood in this region can keep you alive._"

*0*0*

They managed to check several more progressively dirtier levels before they were spotted.

While they had been seen again several times, they had been able to react quickly enough to take down the guards before they raised the alarm.

This time, the two men who spotted them had come out of a concealed doorway directly in front of the trio. Lance launched himself at the first one- tackling him while beating him with the butt of his gun.

The other guard was quicker witted- running back into the room he just exited.

"Intruders! Sound the alar-"

"HISS-THUNK"

The guard stared uncomprehendingly at Jolteon's pin missile now firmly lodged in his chest. He stood for a couple seconds before toppling into his own pool of blood. Michael stepped over the body with Jolteon-

And into a room with several peons and scientists- all of them looking at him with a mixture of horror and fury. The nearest one hit the alarm- completely ruining the element of surprise.

"_So much for an easy mission"._ Michael thought. He dove into cover as the first rounds began pinging off machinery. Several of the scientists pulled out pokeballs.

"Kingler, use Shadow rush!"

"Shadow ball Cacturne!"

"Use thundershock Voltorb!"

Waves of shadow energy joined the deadly hail of bullets. Most pokemon and their trainers wouldn't have the guts to stand up against such a barrage.

Michael and Jolteon were not most trainers. They did not have the bond that most trainers and pokemon had. Their bond had been forged from countless hours drilling together until they were almost one being. There was nothing one wouldn't do for the other.

Michael managed to take out the remaining guards with well-placed shots. He was now left with three scientists who had remained in the area to combat this foe.

"_right, lets show them a taste of their own medicine._" Michael thought. "Jolteon, use thundershock on Kingler!"

"Jolteeee,,,ON!"

Jolteon blasted the shadow pokemon with electrical energy. The water type didn't stand a chance. It frothed and bubbled, but was unable to remain standing. Michael quickly captured it with a snag ball.

"Cacturne, use bullet seed!"

"Cacturne! Cacturne!" tiny seeds began to pelt Jolteon who yelped in pain.

"Jolteon, fight back with a pin missile!"

Jolteon responded and shot hardened bits of his fur at the unfortunate pokemon. Unlike the previous use, Jolteon had purposely taken some of the power out from behind it so that it was nonlethal. Nonetheless, it was still a powerful blow. Within seconds, that pokemon had been captured as well.

Michael turned to the remaining scientist who cowered in a corner with his pokemon.

"Don't take my Voltorb dude! He's my only friend!"

Michael advanced on the man. As he got closer, he was surprised to see that he was just a teenager- not much older than himself. A quick check showed that the voltorb was normal and had no shadow impurity.

"Your Voltorb is normal. Why would I take it?"

"I don't know man, we were told that you stole all pokemon from the trainers- shadow or not! Please don't do it. I don't want to see him hurt!"

Michael realized that he couldn't hurt this guy. Unlike other members of Cipher, this guy actually cared about his pokemon. Even if the Voltorb was a shadow, he doubted he could bring himself to snag it.

"Go". Michael sighed. "Just go and get out of here. This place is going to be rubble soon."

"Wait, Wha-?"

"Go before I change my mind!" Michael yelled. He felt bad for the guy, but he didn't feel like messing with him anymore.

The guy ran out with his Voltorb in close pursuit. Michael turned to the other Scientists.

"If you don't want to go the way of the guards, I'd suggest following suit. Before you go through, do you have any remaining Shadow Pokemon?"

"No sir" one of them whimpered (funny how a gun and 5 dead guards will make a grown man call a teenager "sir"). "We were lucky to get the two we did. Production has ceased all together. The only reason we got any is because they were going to be the test subjects when we finally got the professor to speak."

"You've seen the professor?" Lance inquired. He had a cut to the arm and his cape was torn, but he looked no worse for wear.

The second one gulped. He recognized the caped man in front of him all too well- few didn't.

"Yes sir. We visit him every day when the boss tries to get him to speak."

Michael now had only one question for them.

"Where?"

* * *

**There it is guys! Chapter 3! I originally hoped to get the mission into one chapter, but considering how long this one is already, I think I'll go for two, maybe three. As always, favorite the story if you like it and if you could give me a review, good or bad, I'd like it.**

**Also, I put in a memorial to a character I had to take out. See if you can find it.**

**And finally, I'm thinking about posting a one-shot I had to make for Latin that actually came out pretty cool. The only problem is, I can't think up a name. It's set in the world of Percy Jackson. Any suggestions?**

**Anyways, see you soon!**

**-GN**


	5. And Into The Fire

**I'm back!**

**First of all I'd like to apologize to Fallen Angel Codester for not noticing that you had followed this story until after I posted the last chapter. Completely my bad.**

**Also, you should know that the van I talk about is the van Professor Krane gets kidnapped in. I figured that could confuse some people.**

**ROLL STORY!**

* * *

The captive professor was being held on the 10th floor- 2 floors down from where they were.

"Do you remember this many floors last time?" Lance asked as they raced down the stairs.

"No. I think they've added on since last time." Michael replied.

It was quite apparent that this was the case once they reached the bottom. Excavating equipment lay underneath flickering bare bulbs. The whole place looked like a rough job and completed only recently.

"This place is near bedrock" Lance commented. "The conventional bombing we had planned wouldn't have even touched this place."

They continued for several yards before reaching the cell with the professor in it. Michael, Lance, and Jolteon hid behind several crates to hear the voices coming out of the open door.

"I don't think we're getting anything out of him today Trev'. Let's leave and get some grub."

Michael waited until the guards had left. He then sprinted over to the door and slipped in.

A graying man sat bound and unconscious in a chair behind a metal table. He was bruised and bloodied with dark circles under his eyes. Had it not been for the slow breathing, Michael would have taken him for dead.

Lance slit the tape bonds on the man's wrists and gently lifted him out of the chair.

"We now need to find a way to destroy the base;" Lance said "If we don't, they can come back without too much difficulty. The problem is, I don't think we can do that and keep the professor safe."

Michael knew what had to be done. They had to split up.

"You get going and find us a ride. Jolteon and I will take care of the destruction part."

Lance eyes widened "We can't split up! We don't even know how to destroy this place, let alone get out in time!"

Michael made a shooing gesture with his hands. "Get going Lance. I'm Michael Ryuto; trainer extraordinaire! Jolteon and I will be fine."

Lance started to say something, then stopped. He gave Michael a long look.

"Be careful Michael. I don't want to have to tell your family that you didn't make it."

And with that, he turned around and with the professor over his shoulder, jogged back the way they came. Michael watched him for a second, and then delved deeper in with Jolteon.

*0*0*

Michael had a highly vague idea on what he was going to do. As corrupt as Orre's government was, they couldn't just send a power cable over to a known terrorist organization. It would raise too much suspicion and make the leaders more susceptible to being overthrown.

No, Cipher had to have some sort of generator of their own. Something large enough to power all of this machinery for the 'renovations' and studying pokerus. In Michael's limited experience with generators, they seemed to have a tendency to explode when tinkered with by an untrained teenager.

Michael turned a corner and nearly ran into another pair of Cipher guards. He tackled one of them while Jolteon took down the other with a shockwave. Michael punched the guard twice in quick succession and tore his helmet off. He then stared into the tanned face of his opponent.

"Where is the generator?" Michael demanded. The guard merely spat in his face. Michael hit him in the head with his gun- knocking him out. He then turned to the other guard who was starting to get over being electrocuted. This time, he skipped the beatings and simply pointed his gun at the man's face. "Same question." Michael growled "And you'd better have a different answer." This guard was more than willing to give him directions.

"The reactor is down those stairs and the first door on the left. It has a radioactive symbol on it."

"_Well, that escalated quickly_" thought Michael.

Knocking out this guard too, he and Jolteon jogged down the stairs and through the door. Inside he found the reactor the guard mentioned and a lot of confused scientists. Feeling the need to give the men a chance, he fired a shot in the air and yelled out- "Okay guys, I'm blowing up this here joint! Anyone who doesn't want to die can leave now. Anyone who wants to try and stop me, stick around."

"Don't worry Michael, I'll stay and keep you company" a voice called. A figure came around a bank of computers dressed in black and blue with a horrible sneer.

"Hello Ardos." Michael addressed the current leader of Cipher. "Last I heard, you had been killed when Lance destroyed your main layer. Apparently he was mistaken. Now, if you would be so kind as to step aside, I'll cause a meltdown and we can be on our merry way."

"Like I would ever submit to you." Ardos spat. "You are nothing to Cipher. A miniscule wasp that we will crush into oblivion."

With that, he pulled out a two pokeballs. He threw them to reveal a Tauros and Aerodactyl.

This left Michael in a tough situation. Out of fear for his other pokemon, he had left them at the lab. He had only brought Jolteon with him. While Jolteon could easily take out either of the two separately, two on one odd were not those that he would bet on. Nonetheless, he had to try. Not wasting any time, he had Jolteon start out with a thunderwave. Naturally, fate decided to mess with him as it missed both pokemon.

"My, my, Michael. It looks like your Jolteon isn't up to scratch these days. Aerodactyl, use ancient power and let's see an iron tail Tauros."

Both pokemon sprang into action. Aerodactyl swooped in and let loose its attack while Tauros began whipping its tail back and forth as it prepared to attack.

"Dodge Jolteon, and use a shockwave on Tauros' tail! Then follow up with a thunder on Aerodactyl" Michael called.

Jolteon managed to escape the ancient power and let loose the shockwave- easily hitting the large animal. He then followed up with a thunder.

"Jollltteeeee, ON!"

The room rumbled and roared as a bolt of electricity fell from the ceiling, struck Jolteon, and redirected itself at Aerodactyl. The unfortunate fossil pokemon barely had time to shriek as it was hit by the most powerful move in Jolteon's arsenal. It fell to the floor, twitched twice, and fell unconscious.

The Tauros was luckier. It had taken a glancing hit and was standing back up – albeit shakily. Ardos ignored Aerodactyl for the moment and called out "Get up you big brute! Use takedown on that pest"

Tauros roared and charged at Jolteon. Before the Michael could say anything, the pokemon slammed into Jolteon. Both pokemon went tumbling to the side.

"Jolteon! Quick! Use thunderwave!"

Jolteon responded by shocking the Tauros- paralyzing it. It turned out too much for the Pokemon and it collapsed.

Ardos recalled both pokemon. "That was no victory for you." Ardos sneered. "Those two were pitiful pure pokemon and yet they still dealt damage to yours. Look at it now!"

Michael looked at Jolteon and to his alarm saw he was right. Jolteon was covered in scratches from the rough ground he had skidded on. A shallow gash ran across his flank from one of Tauros' horns.

"Now that he is all tuckered out, I can easily take you down with my next pokemon and then go after that weak champion you call a friend."

He pulled out an ultra-ball and released a massive Charizard with a strange stone around its neck. As he watched in horror, the stone glowed and the pokemon began to morph into a grey beast of a creature. Blue fire emanated from its mouth and from where its tail.

"You see, when we kidnapped the professor, he had some curious notes on him about how if Pokerus was crafted into a stone- like substance, it would cause the pokemon to morph into an even more powerful version. Coupled with the shadow process, this Mega-Charizard is even more powerful than XD001 was before you purified it."

The Charizard roared and charged Jolteon.

*0*0*

To Jolteon's credit, he reacted faster than Michael could speak. He dodged the Charizard's initial swipe and blasted it with thunder. The Charizard roared in pain.

"Charizard, use Shadow fire!"

The beast blasted Jolteon with shadowy fire. Jolteon rolled to the side but was caught in the heat wave of it.

"Jolteon!" Michael cried. The pokemon was struggling to get up and the Charizard wasn't even out of breath.

"You see now boy?" Ardos called. "It is futile to try and fight. With the power of the stone, he is now no longer a fire flying type but is in fact now a fire **dragon** type. As long as we have the stone, you have no advantage. I think a simple shadow rave will do, Charizard."

Knowing he had only seconds, Michael ran towards Jolteon. Diving to protect his friend, he loosed two shots at the pokemon before being hit by the spikes.

*0*0*

Michael hurt. His arms hurt, his legs hurt, his head hurt, come to think of it, he hurt everywhere.

Groaning, he opened his eyes. He was covered in shallow cuts all over his body- courtesy of the shadow attack. Jolteon looked no better, but at least he had been spared the worst of the damage.

Michael then looked over at his opponents. His shots had found their mark- the strange stone around the Charizard's neck was shattered. One of the bullets had gone through and hit it in the neck. Blood was gushing out of the gaping wound.

Michael felt bad. The Charizard wasn't able to control itself and had no power to stop its master. It was now lying battered on the ground.

"Damn you boy!" Ardos yelled. "You've ruined all our work. Now it's almost fainted and useless to us!"

With that statement, Michael knew how he could save the Charizard. He triggered the snag machine and tossed a snag ball at the Charizard. The fire pokemon was almost instantly captured.

Ardos was livid. "HOW DARE YOU STEAL OUR POKEMON! I DON'T CARE IF IT TAKES ALL OF THE REST OF MY POKEMON, I WILL DESTROY YOU!"

Michael knew that this wouldn't be difficult. Jolteon was almost uncosious, and the shadow pokemon he had snagged were too weak to be of any use. This could very well be his end. Seeing his despair, Ardos grinned as he reached for his next pokeball.

"PRIMMMMAAAPPPPPEEEE!"

Both trainers and the pokemon looked in surprise to see a Primape standing on top of the reactor computer with a large explosive in hand. Michael's Aura reader went nuts warning him of the greyish mist that surrounded it instead of the normal shadowy purple. Michael knew what this meant. A downside of the shadow pokemon was that after a few years, they began to regain control of their body yet were unable to open their hearts on their own. The ensuing rage made them difficult to reason with and difficult to capture.

It also made them highly suicidal.

Michael covered himself as the Primape blew itself and the computer to bits. Warning lights began flashing.

"_Warning- warning. Reactor core has become unstable. Meltdown imminent."_

Michael looked at Ardos. The Cipher admin was out cold from the blast. Leaving him, Michael and Jolteon limped away as fast as they could.

*0*0*

Michael and Jolteon thankfully didn't encounter any resistance. A critical nuclear reactor tends to make people worry more about escape than duty. It was there for easy for them to reach the surface where Lance was fending off Cipher members with Dragonite to keep them away from the Cipher getaway van. When he saw Michael and Jolteon, his eyes widened.

"What the hell happened to you two? Is the base set to destroy? Were there any admins there?"

"The reactor is going critical." Michael panted. "we need to leave. **Now.**"

Lance's face paled. Without another word, he got in the cab of the van. Michael dove into the back with Jolteon to rest next to a groaning professor.

The engine started up and they raced away from the laboratory. They had barely gotten 2 miles away when there was a large boom and the laboratory and the surrounding area got swallowed in a giant sinkhole. Few of the Cipher agents managed to escape.

Lance stopped the van and got out. "Holy crap" he muttered "the underground passages must have collapsed when the reactor blew."

"No one underground could have survived" a voice behind them said. Both trainers turned to see the Professor sitting up. "Had you not rescued me along with your mission for destroying the base, I would have died as well. For that, I owe you my life."

Michael shifted uncomfortably. "Umm, sir, our primary objective was changed to getting you out. It wasn't pure coincidence that you were in there."

The man looked at him. "All the same, young man, you saved me and I am in your debt. What is your name?"

Michael Ryuto sir.

That startled the professor "you are the son of the late Professor Joseph Ryuto? Lead scientist on pokemon Aura research and champion of the former Orre Pokemon league?"

"Yes sir."

The professor stuck out his hand. "My name is Professor Samuel Oak. I am honored to meet you."

Michael shook his hand, astounded that he was in the presence of Professor Oak. He was the father of a former league champion and had assisted the current master in achieving his title. That wasn't even mentioning his achievements in the scientific field. Michael felt he should be the honored one.

*0*0*

Lance insisted on getting out of there as soon as possible. The government had a dislike for Michael and had attempted to arrest him on trumped up charges on several occasions. Being near a destroyed laboratory, illegal or not, was tempting fate.

Michael rode in the back with his feet hanging off the side. He was thinking about the mission and while he initially expected to feel satisfaction that it was all over, he instead felt, regret.

"_A lot of people just lost their life today" _Michael thought. "_For six years I have fought and for most of that time, I've had to fight to the death. How much blood is on my hands now? _" He reached over to Jolteon and began scratching him. In less than a week, he would be leaving for Kanto.

In less than a week, he would be away from all of this.

He bowed his head and let the tears flow free- each tear for a person who had died at his hands.

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**CHAPTER 4 GUYS! Sorry it took so long to get this out, but I had a verrryyyy long essay to write for Language arts and this sort of got pushed to the side.**

**Just to clear this up, the Former League champion I mentioned was Oak's grandson in the games, but got moved to being his son to make room for Gary. Apart from that, the story is basically a merging of the anime world, the video game world, and the world I've dreamed up that was influenced by Texas Longhorn's A new Journey (check him out, he's the reason I started this and has a VERY great story going on- even if he takes longer than me at times to post new chapters :P)**

**I also want to mention that the story will be taking a slight turn now. Michael and Jolteon tired of killing and want to get away from the corruption in the Orre region. They're going to try to have a normal life.**

**Also, I posted an oneshot I made for Latin set in the Percy Jackson world. It would make me very happy if some of you guys could check it out and get it more than 18 views.**

**Lastly, i'm looking for a cover image for this story. if anyone is a good artist and would be willing to devote some time to make me a cover for the story, I will love them dearly for it and mention them in the next chapter.**

**As always, please favorite/follow/ review, and I'll be back as soon as possible**

**-GN**


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